Conda installation on Mac not working

[francescodc87]

I am trying to install Trycycler via Conda on a Mac and it is not working..

(trycycler) fxxxxxx@xxxxxx ~ % conda install -c bioconda -c conda-forge trycycler Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: \

It is stuck at the last step for hours

[ctberezin]

I am having a similar issue, and I believe it's due to incompatibilities between new arm64 mac systems and the Edlib package. I get the same error from conda, and here is the tail end of my error from the pip installation route:

Building wheels for collected packages: Trycycler, edlib
  Building wheel for Trycycler (pyproject.toml) ... done
  Created wheel for Trycycler: filename=Trycycler-0.5.4-py3-none-any.whl size=2752908 sha256=d5919d9185aef7f1177ec0b654539a3defbd8104ed97077295e1afdd132f9812
  Stored in directory: /private/var/folders/dk/shj7yjz13jnbrdb6bntm64yh0000gp/T/pip-ephem-wheel-cache-ok9fcpf5/wheels/67/62/7a/7251924133aa18c39f79a6880c2268a475f2ddbe41157199c6
  Building wheel for edlib (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for edlib (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [14 lines of output]
      running bdist_wheel
      running build
      running build_ext
      building 'edlib' extension
      creating build
      creating build/temp.macosx-14.0-arm64-cpython-311
      creating build/temp.macosx-14.0-arm64-cpython-311/edlib
      creating build/temp.macosx-14.0-arm64-cpython-311/edlib/src
      clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Iedlib/include -I/Users/csniffin/.pyenv/versions/3.11.6/include/python3.11 -c edlib.bycython.cpp -o build/temp.macosx-14.0-arm64-cpython-311/edlib.bycython.o -O3 -std=c++11
      edlib.bycython.cpp:198:12: fatal error: 'longintrepr.h' file not found
        #include "longintrepr.h"
                 ^~~~~~~~~~~~~~~
      1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for edlib
Successfully built Trycycler
Failed to build edlib
ERROR: Could not build wheels for edlib, which is required to install pyproject.toml-based projects

There is a related open issue on the edlib github that hasn't received attention since January.

[rrwick]

Frustratingly, the edlib package requires an older version of Python: 3.10 or earlier. So I think if you try installing Trycycler on Python 3.10, it should work, even on an ARM Mac.

I've updated Trycycler on Bioconda to specify Python versions, so hopefully that will help with installation!

Ryan